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Re: blog: semantic dissonance in uniprot

From: Pat Hayes <phayes@ihmc.us>
Date: Wed, 25 Mar 2009 23:25:25 -0500
Cc: "Oliver Ruebenacker" <curoli@gmail.com>, "Phillip Lord" <phillip.lord@newcastle.ac.uk>, "W3C HCLSIG hcls" <public-semweb-lifesci@w3.org>
Message-Id: <359A7A3D-6FE9-4FB1-94A3-2F642E8EBDF6@ihmc.us>
To: Mark Wilkinson <markw@illuminae.com>

On Mar 25, 2009, at 12:13 PM, Mark Wilkinson wrote:

> On Wed, 25 Mar 2009 10:03:43 -0700, Oliver Ruebenacker <curoli@gmail.com 
> > wrote:
>>> http://www.uniprot.org/tissues/229 (subject)
>>> http://www.w3.org/2002/07/owl#sameAs (predicate)
>>> http://purl.uniprot.org/po/0009009 (object)
>>> my concern is whether http://purl.uniprot.org/po/0009009 is  
>>> intended to be a
>>> class, or intended to be an instance... since owl:sameAs is only  
>>> supposed to
>>> be used to claim the "identicalness" of two individuals, not an  
>>> individual
>>> to a class...
>>  Must be an individual, then, doesn't it?
> Well, the statement would *imply* that it is... so given that the  
> individual "embryo" that was referred to as a uniprot tissue is the  
> same individual "embryo" that the plant ontology was talking about,  
> we can therefore conclude that (as Ben pointed-out) that this  
> particular fly embryo is somehow embedded in some particular plant  
> seed endosperm.
> Lovely...
> the problem with owl:sameAs is that it is much more rigourous than  
> most of our ontologies are!  I don't think we need to throw it away,  
> but we need to be ACUTELY aware of what it MEANS, and only use it in  
> those VERY rare cases where we are saying that "Bill Clinton" is  
> owl:sameAs "William Jefferson Clinton" (the example from the OWL spec)

Yes. Look, owl:sameAs is really a very simple idea. Its the same idea  
as the equals sign in mathematics. What A sameAs B, or A=B, means, is  
that there is ONE THING which has two names, 'A' and 'B'. What that  
thing is, its nature, is irrelevant (as is, outside of OWL, whether or  
not it is an 'individual'): whatever the things are that your ontology  
is talking about, the equational or sameAs assertion says that two  
names name one of those. If want to say anything else other than this,  
you really should not use owl:sameAs, because this is one of those  
meanings that really is not open for negotiation.

As this really is very simple, most other intended uses of sameAs  
(which aren't really sameAs) will be something more complicated than  
sameAs. Being very similar to, being indistinguishable from for most  
purposes, being a reasonable stand-in for, being a representative of  
or a surrogate for, having the same conceptualization as, ... ; all of  
these are much more complicated, much less clear notions that will be  
harder to specify and may require their own OWL ontologies (or worse)  
and the making of subtle distinctions. Some of them might need  
original work in philosophical logic. Equality - sameAs - is one of  
the oldest notions in all of formal logic, and is thoroughly  
understood. None of these other ideas has even been considered in any  
depth by anyone, yet.  None of them are going to be delivered on a  
plate by language designers, certainly not in the near future. Sorry.

Pat Hayes

> M
> -- 
> Mark D Wilkinson, PI Bioinformatics
> Assistant Professor, Medical Genetics
> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary  
> Research
> Providence Heart + Lung Institute
> University of British Columbia - St. Paul's Hospital
> Vancouver, BC, Canada

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Received on Thursday, 26 March 2009 04:27:22 UTC

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